valr (version 0.8.4)

bed_merge: Merge overlapping intervals.

Description

Operations can be performed on merged intervals by specifying name-value pairs. Default max_dist of 0 means book-ended intervals are merged.

Usage

bed_merge(x, max_dist = 0, ...)

Value

ivl_df

Arguments

x

ivl_df

max_dist

maximum distance between intervals to merge

...

name-value pairs that specify operations on merged intervals

Details

input tbls are grouped by chrom by default, and additional groups can be added using dplyr::group_by(). For example, grouping by strand will constrain analyses to the same strand. To compare opposing strands across two tbls, strands on the y tbl can first be inverted using flip_strands().

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/merge.html

Other single set operations: bed_cluster(), bed_complement(), bed_flank(), bed_genomecov(), bed_partition(), bed_shift(), bed_slop()

Examples

x <- tibble::tribble(
  ~chrom, ~start, ~end,
  "chr1", 1, 50,
  "chr1", 10, 75,
  "chr1", 100, 120
)

bed_glyph(bed_merge(x))

x <- tibble::tribble(
  ~chrom, ~start, ~end, ~value, ~strand,
  "chr1", 1,      50,   1,      "+",
  "chr1", 100,    200,  2,      "+",
  "chr1", 150,    250,  3,      "-",
  "chr2", 1,      25,   4,      "+",
  "chr2", 200,    400,  5,      "-",
  "chr2", 400,    500,  6,      "+",
  "chr2", 450,    550,  7,      "+"
)

bed_merge(x)

bed_merge(x, max_dist = 100)

# merge intervals on same strand
bed_merge(dplyr::group_by(x, strand))

bed_merge(x, .value = sum(value))